Description

NOTE:
ClinVar is intended for use primarily by physicians and other
professionals concerned with genetic disorders, by genetics researchers, and
by advanced students in science and medicine. While the ClinVar database is
open to all academic users, users seeking information about a personal medical
or genetic condition are urged to consult with a qualified physician for
diagnosis and for answers to personal questions.

This track shows the genomic positions of variants in the
ClinVar database.
ClinVar is a free, public archive of reports
of the relationships among human variations and phenotypes, with supporting
evidence. The track is updated after every ClinVar release, once a month.

Note: The data in the track are obtained directly from ClinVar's FTP site.
We display the data obtained from ClinVar as-is to avoid discrepancies between UCSC and NCBI.
However, be aware that the ClinVar conventions are different from the VCF standard.
Variants may be right-aligned or may contain additional context, e.g. for
inserts. ExAC/gnomAD make available a converter
to make ClinVar more comparable to VCF files.

Display Conventions and Configuration

Genomic locations of ClinVar variants are labeled with the ClinVar variant
descriptions. All information related to each is variant is shown on that
variant's details page. Leave the mouse over a feature for more than 2 seconds
to show the clinical significance of a variant.

The track is divided into two subtracks, one for copy number variants (CNVs), which are all
variants longer than 50bp, and a second track for shorter substitutions and indels.

Until October 2017, all variants with the ClinVar types copy number gain/loss
and DbVar "nsv" accessions were put in the CNV category. Due
to the ClinVar type not capturing this information anymore, anything longer
than 50bp is now considered a CNV.

Entries in the ClinVar CNV track are colored
red for loss and
blue for gain.

Entries in the ClinVar short variants track are shaded by clinical annotation:
red for pathogenic,
dark grey for uncertain significance or not provided and
dark blue for variant of uncertain significance and
light blue for conflicting and
green for benign.

The score of the variants is the number of "stars" in ClinVar. On the track configuration page (above), you can filter the track to show only variants with more than a certain number of stars. For more information on the star rating, see the ClinVar documentation.

For the human genome version hg19: the hg19 genome released by UCSC in 2009 had a
mitochondrial genome "chrM" that was not the same as the one later used for most
databases like ClinVar. As a result, we added the official mitochondrial genome
in 2020 as "chrMT" and all mitochondrial annotations of ClinVar and most other
databases are shown on the mitochondrial genome called "chrMT". For full description
of the issue of the mitochondrial genome in hg19, please see the
README file
on our download site.

Data updates

ClinVar publishes a new release on the
first Thursday every month
and this track is updated automatically at most six days
later. The exact date of our last update is shown when you click onto any variant.
You can find the previous versions of the track organized by month on our
downloads server in the
archive
directory. To access one of these previous versions, paste the URL to one of
the older files into our "Custom tracks" box.

Data access

The raw data can be explored interactively with the Table Browser
or the Data Integrator. The data can be
accessed from scripts through our API, the track names are
"clinVarMain and "clinVarCnv".

For automated download and analysis, the genome annotation is stored in a bigBed file that
can be downloaded from
our download server.
The files for this track are called clinVarMain.bb and clinVarCnv.bb. Individual
regions or the whole genome annotation can be obtained using our tool bigBedToBed
which can be compiled from the source code or downloaded as a precompiled
binary for your system. Instructions for downloading source code and binaries can be found
here.
The tool
can also be used to obtain only features within a given range, e.g.
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb -chrom=chr21 -start=0 -end=100000000 stdout

Methods

ClinVar files were reformatted at UCSC to the bigBed format.
The data is updated every month, one week after the ClinVar release date.
The program that performs the update is available on
Github.

Credits

Thanks to NCBI for making the ClinVar data available on their FTP site as a tab-separated file.